Hierarchical Phase-Contrast Tomography Imaging: Applicability in biomedical research

Docter, D.; Brunet, J.; Sabarigirivasan, V.; Lemmens, G.; Tielemans, B.; Sporring, J.; Dejea, H.; Urban, T.; Purzycka, J.; Gorter, R.; Huirne, J.; Michels, V.; Hanemaaijer-van der Veer, J.; Bellier, A.; Stansby, D.; Ackermann, M.; D. Buelow, R.; Jonigk, D.; Jacob, J.; Hagoort, J.; Verleden, S.; Cook, A.; Walsh, C.; Tafforeau, P.; Lee, P.; de Bakker, B.

doi:10.64898/2026.01.15.699614

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bioRxiv · 10.64898/2026.01.15.699614

Hierarchical Phase-Contrast Tomography Imaging: Applicability in biomedical research

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Abstract

ObjectivesHierarchical Phase-Contrast Tomography (HiP-CT) enables non-destructive, multi-scale imaging of whole human organs. We describe how HiP-CT is utilized for biomedical research within the Human Organ Atlas Hub through three case studies: mapping the enteric nervous system (ENS) of the human colon, analysing myocardial and AV conduction architecture in Tetralogy of Fallot (TOF), and characterizing ductal organization in breast carcinoma. The challenges we faced with this novel biomedical data are discussed. MethodsWhole-organ and region-of-interest scans of three types of human organs were acquired at the European Synchrotron Radiation Facility (ESRF) with isotropic voxel sizes ranging from 20 {micro}m to 0.8 {micro}m. For the colon, voxel binning and RootPainter were employed to tackle data size to segment the ENS. For the heart, voxel-wise myocyte orientation mapping was calculated in terabyte-scale datasets with a high-performance computational framework (Cardiotensor). Breast carcinoma samples were correlated with histopathology for structure validation. ResultsHiP-CT revealed the large-scale organization of the ENS in the colon, enabling visualisation of the 3D structures of the ENS across the colon In TOF hearts, analysis uncovered abnormal myocardial structure and heterogeneous conduction system morphology. In breast carcinoma, HiP-CT resolved the full hierarchy of ductal structures and vascular relationships within tumour and peritumoral regions. ConclusionsHiP-CT provides unprecedented, hierarchical insight into intact human organ structure, bridging the gap between histology and radiology. Advances in knowledgeHiP-CT establishes a new ex vivo radiological modality capable of linking microscale pathology to whole-organ context, advancing translational research in neurogastroenterology, cardiology, and oncology

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Docter, D., Brunet, J., Sabarigirivasan, V., Lemmens, G., Tielemans, B., Sporring, J., Dejea, H., Urban, T., Purzycka, J., Gorter, R., Huirne, J., Michels, V., Hanemaaijer-van der Veer, J., Bellier, A., Stansby, D., Ackermann, M., D. Buelow, R., Jonigk, D., Jacob, J., Hagoort, J., Verleden, S., Cook, A., Walsh, C., Tafforeau, P., Lee, P., de Bakker, B.. 2026-01-19. Hierarchical Phase-Contrast Tomography Imaging: Applicability in biomedical research. https://doi.org/10.64898/2026.01.15.699614

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